I've done both, the full and the empty tank, both worked well for me and no problems with either method. Like Cobram said, you do want to lift the tire off the ground, and make sure its on a solid, waterproof surface to protect from dry rot. Also, like Stitch said, changing the oil and coolant before winter isn't a bad idea. With new oil in you don't have to worry about any water or other contaminants that are in the old oil doing any damage. I leave the brake fluid in and change it at the start of the season, don't know if that makes any difference or not. If you're storing it inside you can put a light dust cover over it (sheet or similar) but if you keep it outside you want to make sure your cover breathes so condensation doesn't hurt the bike. Don't use a standard plastic tarp, get a good, quality cover specifically meant for your bike. I learned that the hard way, I killed my headers by covering it with a non-breathable cover, next spring the headers were beyond a simple sanding and I had to end up painting them black..